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There is a fundamental issue well-known to economists that when a good has negative externalities [wikipedia.org] (e.g., pollution), then the forcing those generating the externalities to internalize those costs is widely considered the fairest way to deal with them. The problem is really trying to assess what those costs actually are and which manufacturers are responsible for which portion of the costs (the devil is always in the details). Since software manufacturers clearly generate a product with negative externalit

A product does not have negative externalities merely because it harms its owner. You can pour diesel in your own fish tank; only when you pour it in the river does it become an externality.

Of course there is harm to society as a whole from the existence of botnets. But some negative effect or another exists for any product from cars to telephones to books. There are many positive effects on society from the use of software, but makers don't get a special subsidy because of them. The quality of the program (including how secure it is) is taken into account by consumers when deciding what to buy and use.

Now, if consumers aren't able to make an informed judgment there may be a case for regulation. But I find it hard to believe that legislators, government agencies and lawyers would make a better judgment than individuals do. Further, even if you disagree with the government's opinion of what software you are allowed to run, there is no way to get around it. For that reason it's best to let individuals make their own choices.